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DRAQ5 is a fluorescent DNA-binding dye used for staining nucleic acids in cells and tissues. It binds to both double-stranded and single-stranded DNA, emitting a strong red fluorescence signal upon binding. DRAQ5 can be used for various applications, including cell cycle analysis, apoptosis detection, and nuclear staining in microscopy and flow cytometry.

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157 protocols using draq5

1

Quantifying EV-derived Amyloid-beta in Recipient Neural Progenitor Cells

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EV-derived Aβ HiLyte fluorescence was quantified in the recipient NPCs using a plate reader. Briefly, NPCs were plated in 96-well black plates (9,000 cells/well) and differentiated for 3 days with the last 24 h in the presence of the isolated EVs. To block Serpine-1 activity, selected NPC cultures were cotreated with 2 μM PAI039 and brain endothelial EVs for 24 h. After treatment, cells were washed with PBS, fixed with ethanol for 30 min at 4°C, washed again with PBS and Aβ HiLyte fluorescence was measured with a plate reader (Molecular Devices, SpectraMax iD3) as suggested by the manufacturer (Anaspec, Ex/Em 503/528 nm). Cell nuclei were stained with DRAQ5 (Cell Signaling, Catalog #4084L, dilution 1:1000) for 5 min, washed with PBS and DRAQ5 fluorescence was measured with the same plate reader (Ex/Em 647/681). Aβ HiLyte fluorescence was then normalized to nuclear DRAQ5 fluorescence.
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2

Screening Nuclear Size Regulators

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For each hit in the nuclear size screen, the two sgRNAs with the highest phenotypic score in the screen and the two sgRNAs with the highest score predicted by the CRISPRi-v2 algorithm (Horlbeck et al., 2016 (link)) were selected and pooled to generate a mixed sgRNA pool of three to four sgRNAs (detailed information in Table S4). Cells (hTERT-RPE1 dCas9-KRAB-BFP PA-mCherry H2B-mGFP) were transduced with pooled sgRNAs targeting each gene and puromycin selected for 2 d to prepare for imaging. Cells were then seeded into 96-well glass-bottom imaging dishes. For DRAQ5 staining experiment, cells were further stained with 5 µM DRAQ5 (Cell Signaling) for 1 h before imaging. Images were collected the next day, and nuclear size and DRAQ5 staining intensity was measured using the Auto-PhotoConverter μManager plugin. To focus on cells with successful transduction, BFP was coexpressed on the sgRNA construct, and only cells with BFP intensity above a threshold value were included in nuclear size measurements. This BFP threshold was established by comparing the average BFP intensity of cells with and without sgRNA transduction (Fig. S3 a).
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3

Multiparameter Imaging Flow Cytometry

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Imaging flow cytometry was performed using the ImageStreamX Mark II imaging flow cytometer (Amnis Corporation) equipped with a 40 × objective, 6 imaging channels, and 405 nm, 488 nm, and 642 lasers. For analysis of cell viability and CD45 expression, the enriched leukocytes were resuspended in 0.1% BSA in HEPES-buffered saline after RBC lysis and stained with the following antibodies and stains where applicable: DRAQ5 (1 μM; Cell Signaling Technologies), Sytox Blue (1 μM; Life Technologies), CellEvent Caspase-3/7 Green Detection Reagent (0.75 μM; Life Technologies), FITC-conjugated CD45 antibody (1:500; clone 5B1; Miltenyi Biotec), PE-conjugated CD66b antibody (1:125; clone G10F5; Stemcell Technologies), and PE-Cy7-conjugated CD16 antibody (1:200 or 1:333; clone 3G8; BD Biosciences). Single cells were gated using the nuclear marker DRAQ5. Neutrophils were identified by the dual positivity of CD66b and CD16. For analysis of neutrophil activation post-enrichment, cells were stained with DRAQ5 (1 μM; Cell Signaling Technologies), VioBlue-conjugated CD45 antibody (1:100; clone 5B1; Miltenyi Biotec), Alexa Fluor 488-conjugated CD11b antibody (1:500; clone ICRF44; Stemcell Technologies), PE-conjugated CD66b antibody (1:125; clone G10F5; Stemcell Technologies), and PE-Cy7-conjugated CD16 antibody (1:333; clone 3G8; BD Biosciences).
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4

Quantifying Amyloid-beta Uptake in Neural Progenitor Cells

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EV-derived Aβ HiLyte fluorescence was quantified in the recipient NPCs using a plate reader. Briefly, NPCs were plated in 96-well black plates (9,000 cells/well) and differentiated for 3 days with the last 24 h in the presence of the isolated EVs. To block Serpine-1 activity, selected NPC cultures were cotreated with 2 μM PAI039 and brain endothelial EVs for 24 h. After treatment, cells were washed with PBS, fixed with ethanol for 30 min at 4 °C, washed again with PBS and Aβ HiLyte fluorescence was measured with a plate reader (Molecular Devices, SpectraMax iD3) as suggested by the manufacturer (Anaspec, Ex/Em 503/528 nm). Cell nuclei were stained with DRAQ5 (Cell Signaling, Catalog #4084L, dilution 1:1000) for 5 min, washed with PBS and DRAQ5 fluorescence was measured with the same plate reader (Ex/Em 647/681). Aβ HiLyte fluorescence was then normalized to nuclear DRAQ5 fluorescence.
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5

3D Co-culture Immunofluorescence Protocol

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The 3D co-cultures were fixed in the μ-angiogenesis wells with 2% paraformaldehyde (PFA) in PBS for 20 min, washed with cold PBS and blocked in 20% horse serum. Cell permeabilization was performed by addition of 0.7% Triton X-100 (Sigma-Aldrich). Fixed cultures were incubated at 4°C overnight with primary antibodies (1:100), washed with PBS and incubated for 3–4 h, at RT with secondary antibodies (1:500) and Draq5 (1:1000, Cell Signaling Technology), to visualize the nuclei and AlexaFluor® 488 Phalloidin (1:50, Life Technologies), to detect F-actin. The following primary antibodies were used: anti-vimentin (SP20) and anti-E-cadherin (HECD-1, both from Abcam), and anti-laminin-α1 (LAM-89, Santa Cruz). Images were taken with the Zeiss Axiovert-200M spinning disc confocal microscope, using a 20x objective. Z-stacks were acquired with a step-size of 8 μm. The images were pre-processed using SlideBook and NIH Image J.
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6

Immunohistochemical Analysis of Bone Markers

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All reagents were purchased from Sigma-Aldrich unless otherwise stated. The following antibodies were obtained from Abcam, MMP13 (39012), osterix (22552), VEGF (46154) and nestin (18102). DRAQ5, NFκB p65 (4764) and nestin (47607) antibodies were purchased from Cell Signalling Technology Inc. WDR33 (374466) and ADAMTS5 (83186) antibodies were purchased from Santa Cruz Biotech. CPSF4 antibody was obtained from Protein Tech. PCNA (M0879) and CD68 (M0814) antibodies were obtained from Dako. Alkaline phosphatase and peroxidase kits as well as secondary antibodies were obtained from Vector Labs. MCSF was obtained from R&D Systems. RANKL was obtained from Peprotech.
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7

Quantitative Analysis of CypD Expression

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Tg CypD+, CypD−, and nonTg mouse brains were fixed by perfusion with 4% paraformaldehyde and coronal sections (30 μm) were cut with a Vibratome (Leica VTS1000, Wetzlar Germany). Sections were collected and immersed in wash buffer (0.1 M sodium phosphate, 0.5 M sodium chloride, 0.1% Triton X-100, pH 7.4) for 1 hour. After preincubation with blocking solution (10% normal goat serum, 0.3% Triton X-100 in PBS , pH 7.4) for one hour at room temperature, sections were co-immunostained with primary antibodies [mouse anti-CypD (Ab110324, 1:500; Abcam) and rabbit anti-SODII (1:5000, ADI-SOD-111, Enzo life Sciences, USA) or rabbit anti-MAP2 (1 : 500, A16657, life technologies, USA) at 4 °C for overnight. Sections were then incubated with Alexa Fluor 594-conjugated goat anti-rabbit IgG and 488 goat anti-mouse IgG secondary antibodies (1 : 1000, Invitrogen) for 1 h at room temperature. Nuclei were stained by DRAQ5 (5 μM, Cell Signaling) for 10 min at room temperature. The staining images were taken under confocal microscopy. Brain sections incubated with non-immune IgG or 2nd antibody alone were used as negative controls. An investigator who was blinded to experimental groups analyzed all images. For quantification of human CypD staining, brain sections were randomly selected and measured using MetaMorph software (Molecular Devices, CA).
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8

Isolation and Characterization of Neutrophils

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Nucleated cells were collected from whole blood via red blood cell sedimentation using HetaSep solution (STEMCELL Technologies, Cat# 07906). Neutrophils were isolated as previously described (plasma centrifuged, PBMCs isolated and collected, and neutrophils isolated from remaining red blood cell pellet). Isolated neutrophils and nucleated cells were centrifuged at 300g for 5 minutes at room temperature with the brakes off. The cells were then resuspended in 50 μl of FACS buffer (0.5% BSA in PBS) and then fixed in 1% paraformaldehyde in PBS. All fixed cells were then stained with CD66b (1:200 dilution) (Biolegend, Cat# 305103), CD14 (1:20 dilution) (Biolegend, Cat# 325615), and DRAQ5 (1:2000 dilution) (Cell Signaling Technology, Cat# 4084S). Data was obtained through the Amnis ImageStreamX Mark II imaging flow cytometer and INSPIRE software (EMD Millipore, Billerica, MA, USA). The accompanying IDEAS software (EMD Millipore) was used to perform data analysis.
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9

Fluorescence Imaging of Membrane Proteins in Arteries

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The expression of membrane-targeted tandem dimer Tomato (mT) and membrane-targeted green fluorescent protein (mG) was assessed by fluorescence microscopy imaging on intact mesenteric artery segments. Mesenteric artery segments were stained with DRAQ5 (1 μmol/l, Cell Signaling Technology, Danvers, Massachusetts, USA) for 20 min to label the nuclei and washed in PBS three times (20min each). Mesenteric arteries were mounted in Fluoromount (Sigma-Aldrich; St. Louis, Missouri, USA) and imaged using a Wave FX Spinning Disc Confocal microscope (Quorum Technologies; Guelph, Ontario, Canada).
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10

Quantification of Reovirus Attachment

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Quantification of reovirus attachment was performed as previously described [38 (link)]. Briefly, NT, ΔCTSL, and ΔWDR81 cells grown in 96-well plates (Greiner Bio-One) were chilled for 15 min at 4°C. The chilled cells were adsorbed with T3DCD at 1.0×106 virions/cell or 1.0×106 ISVPs/cell for 1 h at 4°C. After 1 h, the cells were washed three times with chilled PBS and blocked with PBS supplemented with 5% bovine serum albumin (PBS-BSA) for 10 min at 4°C. The cells were then incubated with an α-reovirus primary antibody [39 (link)] diluted 1:2,500 into PBS-BSA for 30 min at 4°C. The cells were washed three times with PBS-BSA followed by incubation with an IRDye 800CW secondary antibody (LI-COR) diluted 1:1,000 into PBS-BSA for 30 min at 4°C. After two washes with PBS-BSA, total cells were labeled with a 1:1,000 dilution of DRAQ5 (Cell Signaling Technology) for 5 min at 4°C. The cells were washed three times with PBS-BSA and then fixed with 4% formaldehyde for 20 min at room temperature. The fixed plates were scanned using an Odyssey imaging system (LI-COR). The binding index was quantified by the ratio of green (attached virus) and red (total cells) fluorescence using Image Studio Lite software (LI-COR).
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